Jakarta Bay is one of the aquatic ecosystems with the highest level of organic pollution in the world. Ecological condition of Jakarta Bay’s water will affect the ecosystem, including the distribution of heterotrophic bacteria. This study aims to determine the dynamics of the heterotrophic bacteria distribution in the Jakarta Bay. Sampling was conducted four times in 2013. Primary and secondary data was used in this research. The results showed that the abundance of heterotrophic bacteria fluctuated and were relatively high in the area near the mouth of the river and it decreased towards the outer of the bay. The highest abundance was obtained at Station 10 with 3,5 × 106 CFU/ml density and the lowest one was at Station 1 with 1,8 × 105 CFU/ml density. The highest density was obtained in October with an average of 1,3 × 106 CFU/ml and the lowest density was obtained in July with the average of 3,5 × 105 CFU/ml. Abundance of heterotrophic bacteria had strong relationships with chlorophyll-a.